BN0464 Genetic Spatial Mapping Report

Genetic Spatial Mapping Plot

This plot shows the spatial genetic mapping results across different tissues.

Cauchy Combination Result

This table presents the results of the Cauchy combination test, summarizing the genetic associations.

Annotation P Cauchy P Median
Layer 5 1.9576e-06 4.5021e-04
Layer 3 3.1243e-06 7.7389e-03
Layer 4 5.1568e-06 6.5506e-05
WM 1.7756e-05 9.8240e-03
Layer 6 2.5921e-04 3.1852e-03
Layer 2 2.9091e-04 1.7993e-01
Layer 1 9.9923e-01 5.4744e-01

Diagnosis Manhattan Plot

The Manhattan plot shows the association of SNPs with the top associated gene across the genome.

Gene Expression and GSS Distribution

Select a gene to view its expression distribution and gene specificity score (GSS).

Expression Distribution
SNCA Expression Distribution
Gene Specificity Score (GSS)
SNCA GSS Distribution

Top 50 Gene Diagnostic Info

This table lists the top 50 genes based on diagnostic criteria, including the gene specificity score (GSS) and PCC.

Gene Annotation Median GSS PCC
SNCA Layer 5 2.2871 0.6955
QDPR WM 2.3184 0.6284
EPS15 Layer 4 2.4668 0.6144
OMG WM 2.3027 0.6072
SPOCK1 WM 2.6953 0.6056
SLC24A2 Layer 4 3.0859 0.6048
MAPT Layer 5 2.1348 0.6009
TCEAL7 Layer 5 2.4453 0.6006
BCAP31 Layer 4 2.2832 0.5982
INPP5F Layer 4 2.8652 0.5977
EFHD2 Layer 4 3.0527 0.5911
SLC6A15 Layer 5 2.3916 0.5889
ZBTB16 Layer 4 2.9922 0.5856
UBE2Z Layer 5 2.1445 0.5856
PTPRK Layer 4 2.4785 0.5856
DCTN2 Layer 4 2.3555 0.5850
H2AFY Layer 4 2.3086 0.5822
CSNK2B Layer 4 2.1191 0.5822
DHCR24 Layer 5 2.1543 0.5819
MFSD6 Layer 6 2.3340 0.5811
GPRASP1 Layer 4 2.7656 0.5811
GSTO1 Layer 4 2.2773 0.5810
AP2A2 Layer 4 2.5898 0.5808
ELAVL3 Layer 4 2.2715 0.5805
RAP1GDS1 Layer 4 2.2832 0.5804
VPS35 Layer 4 2.3398 0.5795
OAT Layer 4 2.4941 0.5785
DYNC1H1 Layer 5 2.2969 0.5780
CNP WM 2.4297 0.5767
ARL8B Layer 5 2.3604 0.5764
SATB1 Layer 4 3.5742 0.5763
TBR1 Layer 4 2.9531 0.5763
NRSN1 Layer 4 3.0859 0.5760
ABCA3 Layer 4 2.4238 0.5754
SDHB Layer 4 2.3926 0.5754
CANX Layer 5 2.2148 0.5754
LARP1 Layer 5 2.3291 0.5740
CLIP2 WM 2.2520 0.5736
KIF1B Layer 5 2.1250 0.5735
APBA2 Layer 4 2.7852 0.5735
DNAJC6 Layer 4 2.2832 0.5732
ATP5F1C Layer 4 2.3555 0.5731
APBB1 Layer 4 2.1719 0.5728
NAPG Layer 4 2.3340 0.5712
NUAK1 Layer 4 2.7598 0.5709
AKAP6 Layer 4 2.4512 0.5708
NCOA7 Layer 5 2.5781 0.5707
NDUFS2 Layer 5 2.4834 0.5704
EIF1AX Layer 4 2.3086 0.5704
HERC1 Layer 4 2.6133 0.5704

Running Info

Click to view detailed run information and parameters.

gsMap Version: 1.73.0

Parameters:

  • Sample Name: BN0464
  • Trait Name: PD
  • Summary Statistics File: /mnt/data/projects/ASAP/ST/gsMAP/GWAS_nallsEtAl2019_allSamples_allVariants.sumstats.gz
  • HDF5 Path: /mnt/data/projects/ASAP/ST/gsMAP/st_anndata_h5ads/st_adata_BN0464_for_gsmap.h5ad
  • Annotation: smoothed_label_s5
  • Spatial LDSC Save Directory: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN0464/spatial_ldsc
  • Cauchy Directory: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN0464/cauchy_combination
  • Report Directory: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN0464/report/PD
  • gsMap Report File: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN0464/report/PD/BN0464_PD_gsMap_Report.html
  • Gene Diagnostic Info File: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN0464/report/PD/BN0464_PD_Gene_Diagnostic_Info.csv
  • Report Generation Date: 2025-04-11 00:18:11
  • Number of Processes: 10
  • Spending Time: 0h 3m